Align Citrate/succinate antiporter; Citrate carrier; Citrate transporter (characterized)
to candidate BWI76_RS04375 BWI76_RS04375 anion transporter
Query= SwissProt::P0AE74 (487 letters) >FitnessBrowser__Koxy:BWI76_RS04375 Length = 477 Score = 279 bits (714), Expect = 1e-79 Identities = 162/491 (32%), Positives = 264/491 (53%), Gaps = 24/491 (4%) Query: 3 LAKDNIWKLLAPLVVMGVMFLIPVPDGMPPQAWHYFAVFVAMIVGMILEPI--PATAISF 60 + K+ +WKLL + + ++ L P P+G+ AW +++A IVG++++P P + Sbjct: 1 MQKNKLWKLLVIIAIPLLISLFPAPEGLSKLAWVLSGIYLAAIVGLVIKPFAEPVVLLIA 60 Query: 61 IAVTICVIGSNYLLFDAKELADPAFNAQKQALKWGLAGFSSTTVWLVFGAFIFALGYEVS 120 +A ++ V+G+ L D + A L+G+SS T WLVF AF + + ++ Sbjct: 61 VAASMVVVGN---------LGDGSIKAASV-----LSGYSSGTTWLVFSAFTLSAAFVIT 106 Query: 121 GLGRRIALFLVKFMGKRTLTLGYAIVIIDILLAPFTPSNTARTGGTVFPVIKNLPPLFKS 180 GLG+RIA L+ +G TL LGY +D++LAP TPSNTAR GG V P+I ++ S Sbjct: 107 GLGKRIAYILIGKIGSTTLGLGYVTAFLDLILAPATPSNTARAGGIVLPIINSVAVALGS 166 Query: 181 FPNDPSARRIGGYLMWMMVISTSLSSSMFVTGAAPNVLGLEFVSKIAGIQISWLQWFLCF 240 P + SA+R+G YLM + + T +S MF T A N+L L+ + I I++SW W L Sbjct: 167 EP-ERSAKRVGHYLMLNVYMVTKTTSYMFFTAMAGNILALKMIEDICHIKLSWGGWALAA 225 Query: 241 LPVGVILLIIAPWLSYVLYKPEITHSEEVATWAGDELKTMGALTRREWTLIGLVLLSLGL 300 G+I+L++ P ++Y LY PE+ + A ++ +G +T RE L L +L+LG Sbjct: 226 GLPGIIMLLLTPLITYKLYPPELKKVDNKKI-AKAGMEALGPMTLREKMLSCLFVLALGG 284 Query: 301 WVFGSEV-INATAVGLLAVSLMLALHVVPWKDITRYNSAWNTLVNLATLVVMANGLTRSG 359 WVF + +N + V + ++LML L +V W D+ + WNTL+ ++ +++ L++ G Sbjct: 285 WVFSQSLGVNESTVAIGVMALMLVLRIVTWDDVIKNKGGWNTLIWYGGIIGLSSLLSKVG 344 Query: 360 FIDWFAGTMSTHLE-GFSPNATVIVLVLVFYFAHYLFASLSAHTATMLPVILAVGKGIPG 418 F W A + ++ N IV+V + Y FAS SA+ M+PV A+ + G Sbjct: 345 FFLWLADLLKNNISFNGHGNVAFIVIVALSILVRYFFASGSAYIVAMVPV-FAMLANVSG 403 Query: 419 VPMEQLCILLVLSIGIMGCLTPYATGPGVIIYGCGYVKSKDYWRLGAIFGVIYISMLLLV 478 P+ + L+ S G +T Y G +I+G GY K +W +G I ++ + + + Sbjct: 404 APVMLTALALLFSNSYGGMVTHYGGAAGPVIFGVGYNDIKSWWIIGGILALLTFLLQITL 463 Query: 479 G---WPILAMW 486 G W IL W Sbjct: 464 GVWWWEILIAW 474 Lambda K H 0.328 0.142 0.453 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 768 Number of extensions: 50 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 487 Length of database: 477 Length adjustment: 34 Effective length of query: 453 Effective length of database: 443 Effective search space: 200679 Effective search space used: 200679 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory